Hi Sam
Are you asking if it is better to seed from surface compared to volume? If that is your question then seeding from the surface is more accurate for the cortex, and also allows you to take advantage of being able to have the pial surface as a stopping mask for even more accuracy. Of course depending on your application you may or may not need this kind of sub-voxel accuracy.
Cheers
Saad
> On 14 Jun 2019, at 21:22, Sam W. <[log in to unmask]> wrote:
>
> Hello,
>
> I ran recon-all and now I would like to use freesurfer's ROIs as seed and targets in fsl's probtrackx.
> I read online that freesurfer's mri_label2vol tool will create a volume with voxels near the white surface, which could be used for tractography. In the fdt tutorial however the seed and target ROIs consist mostly of gray matter. Is there a particular advantage in using the default output volume from freesurfer's label2vol instead of the whole cortical ROI?
> Thanks!
>
> Best regards,
> Sam
>
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